Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations.     

Interatomic Lennard-Jones potentials of linear and branched alkanes calibrated by Gibbs ensemble simulations for vapor-liquid equilibria

We propose Lennard-Jones potential parameters for interatomic interactions of linear and branched alkanes based on matching the results of Gibbs ensemble simulations of vapor-liquid equilibria to experimental data. The alkane model is similar as in the OPLS-AA, but multiple atom types for carbon based on the number of covalently bonded hydrogen atoms are necessary to accurately reproduce liquid densities and enthalpies of vaporization with the errors of 2.1% and 3.3%, respectively, for hydrocarbons of various chain lengths and structures. We find that the attraction energies of the carbon atoms are almost proportional to the number of covalent hydrogen atoms with each increasing the carbon energy parameter by approximately 0.033 kcal/mol. Though the present force field outperforms the OPLS-AA force field for alkanes we studied, systematic deviations for vapor pressures are still observed with errors of 15%-30%, and critical temperatures are slightly underestimated. We think that these shortcomings are probably due to the inadequacy of the two-parameter Lennard-Jones potential, and especially its behavior at short distances.     

Adsorption and mixing behavior of ethers and alkanes at the solid/liquid interface

The behavior of binary mixtures of linear symmetrical ethers and alkanes adsorbed to a graphite surface from the bulk liquid mixtures is described on the basis of differential scanning calorimetry (DSC) data. Both the ethers and the alkanes are found to form solid monolayers when adsorbed from the liquid. In addition, the monolayer mixing behavior is addressed. The results indicate that there is good, essentially ideal, mixing in the monolayers for ethers and alkanes of the same overall chain length, where the chain length is equal to the total number of carbon and oxygen atoms in the molecule. However, a difference in chain length of more than one atom results in a variation of mixing behavior from nonideal mixing (for long pairs) to phase separation (for short pairs) on the graphite surface. Hence, we conclude that it is the relative chain lengths that control mixing behavior. The results are quantified using a regular solution model with a correction for preferential adsorption. The phase behavior of the mixed monolayers is also compared to the behavior of the bulk. Interestingly, we observe mixtures where the bulk and monolayer behavior are quite different, for example, phase separation in the bulk but essentially ideal mixing in the monolayer for mixtures of ethers and alkanes with the same chain lengths. At present, we attribute this mixing in the monolayer to dilution of the unfavorable ether oxygen-ether oxygen lone pair interactions by the coadsorbed alkanes. In addition, we find evidence for the preferential adsorption of the alkane over the ether. For example, heptane is preferentially adsorbed over dibutyl ether even though it contains two fewer atoms in the molecular chain. This contrasts with the preferential adsorption of alcohols over alkanes reported previously (Messe, L.; Perdigon, A.; Clarke, S. M.; Inaba, A.; Arnold, T. Langmuir 2005, 21, 5085-5093).     

Conformation of alkanes in the gas phase and pure liquids

Monte Carlo (MC) statistical mechanics simulations have been carried out for the homologous alkane series of n-butane through n-dodecane in the gas phase and for the pure liquids at 298 K and 1 atm using the OPLS-AA force field. The study addresses potential cumulative deviations of computed properties and potential conformational differences between the gas phase and pure liquids, for example, from self-solvation in the gas phase. The average errors in comparison with experimental data for the computed densities and heats of vaporization are modest at 0.7% and 6.9%, respectively. Also, the invariant gas and liquid-phase results for average end-to-end distances and percentages of trans conformations for each nonterminal C-C bond assert that the conformer populations are not altered upon transfer from the gas phase to the pure liquid for the n-alkanes in this size range. Average end-to-end distances were also computed from the results of conformational searches and corroborated the MC findings. Quantitatively, the OPLS-AA result for the trans population of the C3-C4 bond in n-undecane is in close agreement with the findings from (13)C NMR experiments. Finally, previous work on determining the shortest n-alkane that does not have an all-trans global energy minimum has been extended. The smallest n-alkane with a hairpin geometry that is lower in energy than the all-trans conformer occurs for C(22)H(46) with OPLS-AA, though with a correction for GG sequences, the true turning point is likely in the C(16)-C(18) range.     

The breakdown of vinyl ethers as a two-center synchronous reaction

The experimental data on the molecular decomposition of vinyl ethers of various structures to alkanes and the corresponding aldehydes or ketones in the gas phase were analyzed using the method of intersecting parabolas. The enthalpies and kinetic parameters of decomposition were calculated for 17 reactions. The breakdown of ethers is a two-center concerted reaction characterized by a very high classical potential barrier to the thermally neutral reaction (180–190 kJ/mol). The kinetic parameters (activation energies and rate constants) of back reactions of the formation of vinyl ethers in the addition of aldehydes or ketones to alkanes were calculated using the method of intersecting parabolas. The factors that influenced the activation energy of the decomposition and formation of ethers were discussed. Quantum-chemical calculations of several vinyl ether decomposition reactions were performed. Ether formation reactions were compared with the formation of unsaturated alcohols as competitive reactions, which can occur in the interaction of carbonyl compounds with alkenes.     

Alcohols,ethers, carbohydrates,and related compounds. I. The MM4 force field for simple compounds

Simple alcohols and ethers have been studied with the MM4 force field. The structures of 13 molecules have been well fit using the MM4 force field. Moments of inertia have been fit with rms percentage errors as indicated: 18 moments for ethers, 0.28%; 21 moments for alcohols, 0.22%. Rotational barriers and conformational equilibria have also been examined, and the experimental and ab initio results are reproduced substantially better with MM4 than they were with MM3. Much of the improvement comes from the use of additional interaction terms in the force constant matrix, of which the torsion-bend and torsion-torsion are particularly important. Induced dipoles are included in the calculation, and dipole moments are reasonably well fit. It has been possible for the first time to fit conformational energetic data for both open chain and cyclic alcohols (e.g., propanol and cyclohexanol) with the same parameter set. For vibrational spectra, over a total of 82 frequencies, the rms error is 27 cm(-1), as opposed to 38 cm(-1) with MM3. Both the alpha and beta bond shortening resulting from the presence of the electronegative oxygen atom in the molecule are well reproduced. The electronegativity of the oxygen is sufficient that one must also include not only the alpha and beta electronegativity effects on bond lengths, but also on angle distortions, if structures are to be well reproduced. The heats of formation of 32 alcohols and ethers were fit overall to within experimental error (weighted standard deviation error 0.26 kcal/mol).     

顶空气相色谱-质谱法同时测定蜂蜜中57种挥发性有机溶剂残留

建立了顶空气相色谱-质谱(HS-GC/MS)同时测定蜂蜜中57种挥发性有机溶剂(包括烷烃类、芳香烃类、醇类、酮类、酯类、醚类)残留量的分析方法。蜂蜜样品在密封的顶空瓶中用水溶解后,在顶空仪中于80 ℃下平衡30 min,使气-液两相达到动态平衡。采用DB-624毛细管色谱柱(60 m×0.25 mm×1.40 μm)对57种有机溶剂进行分离,GC/MS测定,外标法定量。该方法对于烷烃类、芳香烃类和醚类挥发性有机溶剂在0.005～0.2 μg、酯类0.05～2.0 μg、酮类0.5～20 μg、醇类2.5～100 μg范围内线性关系良好,相关系数均大于0.996。对于烷烃类、芳香烃类和醚类挥发性有机溶剂在1.0～20 μg/kg、酯类10～200 μg/kg、酮类100～2000 μg/kg、醇类500～10000 μg/kg添加范围内的平均添加回收率为61.0%～113.1%,相对标准偏差为1.9%～9.8%。对于烷烃类、芳香烃类和醚类挥发性有机溶剂的检出限为1.0 μg/kg、酯类10 μg/kg、酮类100 μg/kg、醇类500 μg/kg。该方法操作简单、快速,灵敏度和准确度高,适用于蜂蜜样品中多种挥发性有机溶剂残留量的同时检测。     

A new equation for the thermal conductivity of organic compounds

This work presents a wide literature survey of the available data of the experimental thermal conductivity data of organic liquids. The experimental data were collected for 136 compounds belonging to the following families: refrigerants, alkanes, alkenes, aromatics, cycloalkanes, cycloalkenes, ethers, esters, ketones, carboxylic acids, and alcohols. The experimental data were regressed with the most reliable semi-empirical correlating methods existing in the literature and a reliable set of 4,584 experimental data was finally selected. The influence of several physical parameters on the thermal conductivity calculation is discussed and a new equation to represent the thermal conductivity of organic liquids at atmospheric pressure for temperatures below normal boiling point and at saturation for temperatures above the normal boiling point is presented. To minimize the deviation between the predictions and the experimental data and to find the optimal coefficients for the proposed equation, a statistical analysis was performed. The resulting equation is simple and is able to predict the thermal conductivities with low deviations for the major part of the collected data for the studied families.     

Retention in gas-liquid chromatography with a polyethylene oxide stationary phase: molecular simulation and experiment

Configurational-bias Monte Carlo simulations in the isobaric-isothermal Gibbs ensemble were carried out to investigate the partitioning of normal alkanes, primary and secondary alcohols, symmetric alkyl ethers and arenes between a helium vapor phase and a polyethylene oxide stationary phase (M(W)=382 g mol(-1)). The united-atom version of the transferable potentials for phase equilibria force field was used to model all solutes, polyethylene oxide and helium. The Gibbs free energies of transfer and Kovats retention indices of the solutes were calculated directly from the partition constants at two different temperatures, 353 and 393 K. Chromatographic experiments on a Carbowax 20M retentive phase were performed for the same set of solutes and temperatures ranging from 333 to 413 K. The predicted retention indices for alcohols, ethers and arenes are overestimated by about 120, 70 and 20 retention index units, respectively, pointing to an overestimation of the first-order electrostatic interactions in the model system. Molecular-level analysis shows that hydrogen-bonding and dipole-dipole interactions lead to orientational ordering for the alcohol and ether analytes, whereas the weaker dipole-quadrupole interactions for the arene solutes are not sufficient to induce orientational ordering. The retention indices of alcohols and ethers decrease with increasing temperature because of the large entropic cost of hydrogen-bonding and orientational ordering. In contrast, the retention indices for arenes increase with increasing temperature because the entropic cost of cavity formation is smaller for arenes than for comparable alkanes.     

Structural relaxation time for various liquids

The structural relaxation time for series of various liquids (alkanes, aliphatic alcohols, and diols) are calculated from published data on the shear viscosity and the heat of evaporation per unit volume. Liquids having a 3D H-bond network (diols) are characterized by relaxation times one to two orders of magnitudes longer than those typical of liquids without such a network (alkanes and aliphatic alcohols).     

Prediction of phase equilibrium in mixtures containing ionic liquids using UNIFAC

The UNIFAC model is extended to mixtures of ionic liquids consisting of the imidazolium cation and the hexafluorophosphate anion with alkanes, cycloalkanes, alcohols and water. Two new main groups, the imidazolium and the hexafluorophosphate groups, are introduced in UNIFAC. The required group interaction parameters between these groups and the existing UNIFAC main groups, CH₂, OH and H₂O, are determined by fitting binary liquid–liquid equilibrium and infinite dilution activity coefficient experimental data. The predictive capability of the extended UNIFAC model is examined against experimental data for vapour–liquid equilibrium, liquid–liquid equilibrium and activity coefficients at infinite dilution of binary and ternary systems containing 1-alkyl-3-alkyl′-imidazolium hexafluorophosphate ionic liquids, alkanes, cycloalkanes, alcohols and water. The results indicate that UNIFAC is a reliable model for phase equilibrium predictions in mixtures containing this type of ionic liquids.     

Conformational sensitivity analysis of FKBP–FK506/rapamycin complexes

Sensitivity analysis techniques are applied to the FKBP–FK506 and FKBP–rapamycin complexes to quantify the conformational relationships between FKBP and its ligands. Crystal structures of the two FKBP complexes are energy minimized in the Amber force field using a continuum solvent model, and derived Green's function sensitivity coefficients are developed to describe the relationship between the ?, ψ, and χ₁ torsional angles of the FKBP residues and the bound ligand macrocycle torsional angles. Sensitivity analysis is applied to the entire FKBP structure and reveals that the local conformation of the residues of the 80s and 50s loops and of the active site are sensitive to the ligand conformation. The analysis also reveals that the torsional angles controlling the orientation of the amide and keto carbonyls of FK506 are sensitive to the aromatic side chains in the FKBP carbonyl binding pocket. © 1994 by John Wiley & Sons, Inc.     

Biosynthesis of the allylmalonyl-CoA extender unit for the FK506 polyketide synthase proceeds through a dedicated polyketide synthase and facilitates the mutasynthesis of analogues

The allyl moiety of the immunosuppressive agent FK506 is structurally unique among polyketides and critical for its potent biological activity. Here, we detail the biosynthetic pathway to allylmalonyl-coenzyme A (CoA), from which the FK506 allyl group is derived, based on a comprehensive chemical, biochemical, and genetic interrogation of three FK506 gene clusters. A discrete polyketide synthase (PKS) with noncanonical domain architecture presumably in coordination with the fatty acid synthase pathway of the host catalyzes a multistep enzymatic reaction to allylmalonyl-CoA via trans-2-pentenyl-acyl carrier protein. Characterization of this discrete pathway facilitated the engineered biosynthesis of novel allyl group-modified FK506 analogues, 36-fluoro-FK520 and 36-methyl-FK506, the latter of which exhibits improved neurite outgrowth activity. This unique feature of FK506 biosynthesis, in which a dedicated PKS provides an atypical extender unit for the main modular PKS, illuminates a new strategy for the combinatorial biosynthesis of designer macrolide scaffolds as well as FK506 analogues.     

OPLS all-atom force field for carbohydrates

The OPLS all-atom (AA) force field for organic and biomolecular systems has been expanded to include carbohydrates. Starting with reported nonbonded parameters of alcohols, ethers, and diols, torsional parameters were fit to reproduce results from ab initio calculations on the hexopyranoses, α,β-d -glucopyranose, α,β-d -mannopyranose, α,β-d -galactopyranose, methyl α,β-d -glucopyranoside, and methyl α,β-d -mannopyranoside. In all, geometry optimizations were carried out for 144 conformers at the restricted Hartree–Fock (RHF)/6–31G* level. For the conformers with a relative energy within 3 kcal/mol of the global minima, the effects of electron correlation and basis-set extension were considered by performing single-point calculations with density functional theory at the B3LYP/6–311+G** level. The torsional parameters for the OPLS-AA force field were parameterized to reproduce the energies and structures of these 44 conformers. The resultant force field reproduces the ab initio calculated energies with an average unsigned error of 0.41 kcal/mol. The α/β ratios as well as the relative energies between the isomeric hexopyranoses are in good accord with the ab initio results. The predictive abilities of the force field were also tested against RHF/6–31G* results for d -allopyranose with excellent success; a surprising discovery is that the lowest energy conformer of d -allopyranose is a β anomer. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1955–1970, 1997     

An improved OPLS-AA force field for carbohydrates

This work describes an improved version of the original OPLS-all atom (OPLS-AA) force field for carbohydrates (Damm et al., J Comp Chem 1997, 18, 1955). The improvement is achieved by applying additional scaling factors for the electrostatic interactions between 1,5- and 1,6-interactions. This new model is tested first for improving the conformational energetics of 1,2-ethanediol, the smallest polyol. With a 1,5-scaling factor of 1.25 the force field calculated relative energies are in excellent agreement with the ab initio-derived data. Applying the new 1,5-scaling makes it also necessary to use a 1,6-scaling factor for the interactions between the C4 and C6 atoms in hexopyranoses. After torsional parameter fitting, this improves the conformational energetics in comparison to the OPLS-AA force field. The set of hexopyranoses included in the torsional parameter derivation consists of the two anomers of D-glucose, D-mannose, and D-galactose, as well as of the methyl-pyranosides of D-glucose, D-mannose. Rotational profiles for the rotation of the exocyclic group and of different hydroxyl groups are also compared for the two force fields and at the ab initio level of theory. The new force field reduces the overly high barriers calculated using the OPLS-AA force field. This leads to better sampling, which was shown to produce more realistic conformational behavior for hexopyranoses in liquid simulation. From 10-ns molecular dynamics (MD) simulations of alpha-D-glucose and alpha-D-galactose the ratios for the three different conformations of the hydroxymethylene group and the average (3)J(H,H) coupling constants are derived and compared to experimental values. The results obtained for OPLS-AA-SEI force field are in good agreement with experiment whereas the properties derived for the OPLS-AA force field suffer from sampling problems. The undertaken investigations show that the newly derived OPLS-AA-SEI force field will allow simulating larger carbohydrates or polysaccharides with improved sampling of the hydroxyl groups.     

Molecular force field for ionic liquids III: imidazolium, pyridinium, and phosphonium cations; chloride, bromide, and dicyanamide anions

This is the third set of parameters of a force field for the molecular simulation of ionic liquids, developed within the spirit of the OPLS-AA model and thus oriented toward the calculation of equilibrium thermodynamic and structural properties. The parameter sets reported here concern the cations alkylimidazolium, tetra-alkylphosphonium, and N-alkylpyridinium, and the anions chloride, bromide, and dicyanamide. The force field is built in a stepwise manner that allows the construction of models for an entire family of cations, with alkyl side chains of different length, for example. Due to the transferability of the present force field, the ions studied here can be combined with those reported in our two previous publications to create a large variety of ionic liquids that can be studied by molecular simulation. The parameters reported were obtained through different series of ab initio calculations concerning the geometry, force constants, torsion energy profiles, and electrostatic charge distributions of the ions under study. Validation of the force field consisted of comparison with experimental crystal structure and liquid density data.     

Consistent Force Fields for Saccharides

ABSTRACT

Consistent force fields for carbohydrates were hitherto developed by extensive optimization of potential energy function parameters on experimental data and on ab initio results. A wide range of experimental data is used: internal structures obtained from gas phase electron diffraction and from x-ray and neutron diffraction, vibrational frequencies, dipole moments, unit cell dimensions and lattice energies. The range of model compounds covered so far includes alkanes, ethers, alcohols, ketones and mono- and disaccharides. Electrostatic interactions are handled by fractional charges assigned to individual atoms. Charges are modeled such that Mulliken population analyses are reproduced. Morse functions are used for all bonded interactions; experimentally derived dissociation energies are used as parameters. Van der Waals interactions are modeled with Lennard-Jones 12-6 functions. The anomeric and exo-anomeric effects are accounted for without addition of specific terms. The work is done in the framework of the Consistent Force Field which originated in Israel and was further developed in Denmark. The actual methods and strategies employed have been described previously. Extensive testing of the force field is reported, and ways and means of improvement are indicated. Principles of mapping of conformational space are discussed, and a discussion on which properties to preferentially reproduce in modeling is invited.     

An all-atom force field for metallocenes

A new all-atom force field, for the molecular modeling of metallocenes was constructed. Quantum chemical calculations were performed to obtain several force field terms not yet defined in the literature. The remainder were transferred from the OPLS-AA/AMBER framework. The parametrization work included the obtention of geometrical parameters, torsion energy profiles, and distributions of atomic charges that blend smoothly with the OPLS-AA specification for a variety of organic molecular fragments. Validation was carried out by comparing simulated and experimental data for five different ferrocene derivatives in the crystalline phase. The present model can be regarded as a step toward a general force field for metallocenes, built in a systematic way, easily integrated with OPLS-AA, and transferable between different metal-ligand combinations.     

Gas‐phase and liquid‐state properties of esters,nitriles, and nitro compounds with the OPLS‐AA force field

Nonbonded and torsional parameters for carboxylate esters, nitriles, and nitro compounds have been developed for the OPLS‐AA force field. In addition, torsional parameters for alkanes have been updated. These parameters were fit to reproduce ab initio gas‐phase structures and conformational energetics, experimental condensed‐phase structural and thermodynamic properties, and experimental free energies of hydration. The computed densities, heats of vaporization, and heat capacities for fifteen liquids are in excellent agreement with experimental values. The new parameters permit accurate molecular modeling of compounds containing a wider variety of functional groups, which are common in organic molecules and drugs. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1340–1352, 2001     

Study of the effect of Wuzhi tablet (Schisandra sphenanthera extract) on tacrolimus tissue distribution in rat by liquid chromatography tandem mass spectrometry method

A liquid chromatography/tandem mass spectrometry (LC‐MS/MS) method was developed and validated for determining tacrolimus (FK506) in rat tissues to study the effect of Schisandra sphenanthera extract on FK506 tissue distribution. After a liquid–liquid extraction with ethyl acetate, FK506 and ascomycin (IS) were subjected to LC‐MS/MS analysis using positive electrospray ionization under multiple reactions monitoring mode. Chromatographic separation of FK506 and ascomycin was achieved on a Hypersil BDS C₁₈ column with a mobile phase consisting of methanol‐water (containing 2 mM ammonium acetate, 95 : 5, v/v). The intra‐ and inter‐batch precision of the method were less than 8.8 and 9.8%, respectively. The intra‐ and inter‐batch accuracies ranged from 97.5 to 104.0%. The lowest limit of quantification for FK506 was 0.5 ng/mL. The method was applied to a FK506 tissue distribution study with or without a dose of Wuzhi (WZ) tablet. Most of the FK506 tissue concentrations were slightly increased after a concomitant WZ tablet dose, but the whole blood concentration of FK506 was dramatically increased 3‐fold after a concomitant WZ tablet dose. These results indicated that the LC‐MS/MS method was rapid and sensitive enough to quantify FK506 in different rat tissues, and strict drug monitoring is recommended when co‐administering WZ tablet in clinical use. Copyright © 2009 John Wiley & Sons, Ltd.